Python readers.BaseEventReader类代码示例

    def test_as_dataframe(self):
        ber = BaseEventReader(filename=self.filename)
        events = ber.as_dataframe()
        assert isinstance(events, pd.DataFrame)

        with open(self.filename) as f:
            assert len(events) == len(json.loads(f.read()))

def test_2_old():
    import time
    start = time.time()

    e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'

    from ptsa.data.readers import BaseEventReader

    base_e_reader = BaseEventReader(event_file=e_path, eliminate_events_with_no_eeg=True, use_ptsa_events_class=False)

    base_e_reader.read()

    base_events = base_e_reader.get_output()

    base_events = base_events[base_events.type == 'WORD']

    # selecting only one session
    base_events = base_events[base_events.eegfile == base_events[0].eegfile]

    from ptsa.data.readers.TalReader import TalReader
    tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
    tal_reader = TalReader(tal_filename=tal_path)
    monopolar_channels = tal_reader.get_monopolar_channels()
    bipolar_pairs = tal_reader.get_bipolar_pairs()

    print 'bipolar_pairs=', bipolar_pairs

    from ptsa.data.experimental.TimeSeriesEEGReader import TimeSeriesEEGReader

    time_series_reader = TimeSeriesEEGReader(events=base_events, start_time=0.0,
                                             end_time=1.6, buffer_time=1.0, keep_buffer=True)

    base_eegs = time_series_reader.read(channels=monopolar_channels)

    # base_eegs = base_eegs[:, 0:10, :]
    # bipolar_pairs = bipolar_pairs[0:10]


    wf = MorletWaveletFilter(time_series=base_eegs,
                             freqs=np.logspace(np.log10(3), np.log10(180), 2),
                             # freqs=np.array([3.]),
                             output='power',
                             # resamplerate=50.0
                             )

    pow_wavelet, phase_wavelet = wf.filter()

    print 'total time = ', time.time() - start

    res_start = time.time()

    # from ptsa.data.filters.ResampleFilter import ResampleFilter
    # rsf = ResampleFilter (resamplerate=50.0)
    # rsf.set_input(pow_wavelet)
    # pow_wavelet = rsf.filter()



    print 'resample_time=', time.time() - res_start
    return pow_wavelet

    def read_events(self, task, subject):
        e_path = join(self.prefix, 'data/events/%s/%s_events.mat' % (task, subject))

        base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)

        base_events = base_e_reader.read()
        return base_events

 def test_missing_data_read(self):
     self.e_path = '/Volumes/rhino_root/data/events/RAM_PS/R1104D_events.mat'
     if sys.platform.startswith('win'):
         self.e_path = 'D:/data/events/RAM_PS/R1104D_events.mat'
     base_e_reader = BaseEventReader(filename=self.e_path)
     base_events = base_e_reader.read()
     print('base_events=',base_events)

def get_ltp_subject_sessions_by_experiment(experiment):
    events_dir = os.path.join(paths.data_root, 'scalp', 'ltp', experiment, 'behavioral', 'events')
    events_files = sorted(glob.glob(os.path.join(events_dir, 'events_all_LTP*.mat')),
                          key=lambda f: f.split('_')[:-1])
    seen_experiments = defaultdict(list)
    for events_file in events_files:
        print(events_file)
        subject = os.path.basename(events_file)[11:-4]  # Subject number is the basename with events_all_, .mat removed
        subject_no_year = subject.split('_')[0]
        if '_' in subject:
            continue
        mat_events_reader = BaseEventReader(filename=events_file, common_root=paths.data_root)
        logger.debug('Loading matlab events {exp}: {subj}'.format(exp=experiment, subj=subject))
        try:
            mat_events = mat_events_reader.read()
            sessions = np.unique(mat_events['session']) - 1  # MATLAB events start counting sessions at 1 instead of 0
            version = 0.
            for i, session in enumerate(sessions):
                if 'experiment' in mat_events.dtype.names:
                    experiments = np.unique(mat_events[mat_events['session'] == session]['experiment'])
                else:
                    experiments = [experiment]
                for this_experiment in experiments:
                    n_sessions = seen_experiments[subject_no_year].count(this_experiment)
                    yield subject_no_year, subject, n_sessions, session, this_experiment, version
                    seen_experiments[subject_no_year].append(this_experiment)
        except IndexError or AttributeError:
            traceback.print_exc()
            logger.error('Could not get session from {}'.format(events_file))

    def setUp(self):
        self.start_time = -0.5
        self.end_time = 1.6
        self.buffer_time = 0.5

        self.event_range = range(0, 30, 1)

        # here = osp.abspath(osp.dirname(__file__))
        here = get_rhino_root()
        self.e_path = osp.join(here, 'data', 'events', 'RAM_FR1', 'R1060M_events.mat')
        tal_path = osp.join(here, 'data', 'eeg', 'R1060M', 'tal', 'R1060M_talLocs_database_bipol.mat')

        tal_reader = TalReader(filename=tal_path)
        self.monopolar_channels = tal_reader.get_monopolar_channels()
        self.bipolar_pairs = tal_reader.get_bipolar_pairs()

        base_e_reader = BaseEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)
        base_events = base_e_reader.read()
        base_events = base_events[base_events.type == 'WORD']
        base_ev_order = np.argsort(base_events, order=('session', 'list', 'mstime'))
        self.base_events = base_events[base_ev_order]

        # retaining first session
        dataroot = self.base_events[0].eegfile
        self.base_events = self.base_events[self.base_events.eegfile == dataroot]
        self.base_events = self.base_events[self.event_range]

        eeg_reader = EEGReader(events=self.base_events, channels=self.monopolar_channels,
                               start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)

        self.base_eegs = eeg_reader.read()

        session_reader = EEGReader(session_dataroot=dataroot, channels=self.monopolar_channels)
        self.session_eegs = session_reader.read()

    def run(self):
        events = None
        if self.params.include_fr1:
            try:
                e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_FR1', self.pipeline.subject + '_math.mat')
                e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
                events = e_reader.read()
                print "Got FR1 events"
            except IOError:
                pass

        if self.params.include_catfr1:
            try:
                e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_CatFR1', self.pipeline.subject + '_math.mat')
                e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
                catfr1_events = e_reader.read()
                print "Got CatFR1 events"
                if events is None:
                    events = catfr1_events
                else:
                    print "Joining FR1 and CatFR1"
                    catfr1_events.session = -catfr1_events.session-1
                    fields = list(set(events.dtype.names).intersection(catfr1_events.dtype.names))
                    events = np.hstack((events[fields],catfr1_events[fields])).view(np.recarray)
            except IOError:
                pass

        events = events[events.type == 'PROB']

        print len(events), 'PROB events'

        self.pass_object('control_events', events)

    def test_read_json(self):
        ber = BaseEventReader(filename=self.filename)
        events = ber.read_json()
        assert isinstance(events, np.recarray)

        with open(self.filename) as f:
            assert len(events) == len(json.loads(f.read()))

    def setUp(self):
        root = get_rhino_root()
        self.e_path = osp.join(root, 'data', 'events', 'RAM_FR1',
                               'R1060M_events.mat')
        tal_path = osp.join(root, 'data', 'eeg', 'R1060M', 'tal',
                            'R1060M_talLocs_database_bipol.mat')

        base_e_reader = BaseEventReader(filename=self.e_path,
                                        eliminate_events_with_no_eeg=True)

        self.base_events = base_e_reader.read()

        tal_reader = TalReader(filename=tal_path)
        self.monopolar_channels = tal_reader.get_monopolar_channels()
        self.bipolar_pairs = tal_reader.get_bipolar_pairs()

        self.base_events = self.base_events[self.base_events.type == 'WORD']

        # retaining first session
        dataroot = self.base_events[0].eegfile
        self.base_events = self.base_events[self.base_events.eegfile == dataroot]

        eeg_reader = EEGReader(events=self.base_events, channels=self.monopolar_channels,
                               start_time=0.0, end_time=1.6, buffer_time=1.0)

        self.base_eegs = eeg_reader.read()

    def run(self):
        events = None
        if self.params.include_fr1:
            try:
                e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_FR1', self.pipeline.subject + '_events.mat')
                e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
                events = e_reader.read()
                ev_order = np.argsort(events, order=('session','list','mstime'))
                events = events[ev_order]
            except IOError:
                pass

        if self.params.include_catfr1:
            try:
                e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_CatFR1', self.pipeline.subject + '_events.mat')
                e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
                catfr1_events = e_reader.read()
                ev_order = np.argsort(catfr1_events, order=('session','list','mstime'))
                catfr1_events = catfr1_events[ev_order]
                if events is None:
                    events = catfr1_events
                else:
                    catfr1_events.session += 100
                    fields = list(set(events.dtype.names).intersection(catfr1_events.dtype.names))
                    events = np.hstack((events[fields],catfr1_events[fields])).view(np.recarray)
            except IOError:
                pass

        events = events[events.type == 'WORD']

        print len(events), 'WORD events'

        self.pass_object('FR_events', events)

def get_events():
    # ---------------- NEW STYLE PTSA -------------------
    base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)

    base_events = base_e_reader.read()

    base_events = base_events[base_events.type == 'WORD']
    return base_events

    def __init__(self, **kwds):
        BaseEventReader.__init__(self, **kwds)

        if self.eeg_fname_search_pattern != '' and self.eeg_fname_replace_pattern != '':

            self.alter_eeg_path_flag = True

        else:
            self.alter_eeg_path_flag = False

def main_fcn():
    e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'

    from ptsa.data.readers import BaseEventReader

    base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)

    base_events = base_e_reader.read()



    base_events = base_events[base_events.type == 'WORD']

    # selecting only one session
    base_events = base_events[base_events.eegfile == base_events[0].eegfile]

    from ptsa.data.readers.TalReader import TalReader

    tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
    tal_reader = TalReader(filename=tal_path)
    monopolar_channels = tal_reader.get_monopolar_channels()
    bipolar_pairs = tal_reader.get_bipolar_pairs()

    print('bipolar_pairs=', bipolar_pairs)


    from ptsa.data.readers.EEGReader import EEGReader

    sessions = np.unique(base_events.session)
    dataroot = base_events[0].eegfile

    session_reader = EEGReader(session_dataroot=dataroot, channels=monopolar_channels)
    session_eegs = session_reader.read()

    m2b = MonopolarToBipolarMapper(time_series=session_eegs, bipolar_pairs=bipolar_pairs)
    session_bp_eegs = m2b.filter()





    time_series_reader = EEGReader(events=base_events, channels=monopolar_channels, start_time=0.0,
                                             end_time=1.6, buffer_time=1.0)


    base_eegs = time_series_reader.read()


    m2b = MonopolarToBipolarMapper(time_series=base_eegs, bipolar_pairs=bipolar_pairs)
    ts_filtered = m2b.filter()

    del base_eegs
    del time_series_reader

    print()

    pass

    def setUp(self):
        self.event_range = range(0, 30, 1)
        self.e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
        self.tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'

        if sys.platform.startswith('win'):
            self.e_path = 'D:/data/events/RAM_FR1/R1060M_events.mat'
            self.tal_path = 'D:/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'

        # --------------- TAL STRUCTS READ
        tal_reader = TalReader(filename=self.tal_path)
        self.monopolar_channels = tal_reader.get_monopolar_channels()


        # ---------------- ORIG PTSA -------------------
        e_reader = PTSAEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)
        events = e_reader.read()

        events = events[events.type == 'WORD']

        events = events[self.event_range]

        ev_order = np.argsort(events, order=('session','list','mstime'))
        self.events = events[ev_order]

        # self.events = self.read_ptsa_events()

        # in case fancy indexing looses Eventness of events we need to create Events object explicitely
        if not isinstance(self.events, Events):
            self.events = Events(self.events)

        start_time = 0.0
        end_time = 1.6
        buffer_time = 1.0

        self.eegs = self.events.get_data(channels=['002', '003'], start_time=start_time, end_time=end_time,
                                         buffer_time=buffer_time, eoffset='eegoffset', keep_buffer=True,
                                         eoffset_in_time=False, verbose=True)

        # ---------------- NEW STYLE PTSA -------------------
        base_e_reader = BaseEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)

        base_events = base_e_reader.read()

        base_events = base_events[base_events.type == 'WORD']

        base_ev_order = np.argsort(base_events, order=('session','list','mstime'))
        base_events = base_events[base_ev_order]

        self.base_events = base_events[self.event_range]

        # self.base_events = self.read_base_events()

        eeg_reader = EEGReader(events=self.base_events, channels=np.array(['002', '003']),
                               start_time=start_time, end_time=end_time, buffer_time=buffer_time)

        self.base_eegs = eeg_reader.read()

def get_suffixes(subject):
    events_file= os.path.join(DATA_ROOT, '..', 'events', 'RAM_PS', '{}_events.mat'.format(subject))
    mat_events_reader = BaseEventReader(filename=events_file, common_root=DATA_ROOT)
    mat_events = mat_events_reader.read()
    sessions = np.unique(mat_events.session)
    suffixes = {}
    for session in sessions:
        sess_events = mat_events[mat_events.session == session]
        eegfile = sess_events[10].eegfile
        suffixes[session] =  '_'.join(eegfile.split('_')[-2:])
    return suffixes